How do quotes affect command substitution?

Quotes can significantly affect command substitution by controlling how the output of a command is treated, particularly with respect to whitespace and special characters.

Double Quotes ("): When you use double quotes around a command substitution, the output retains its whitespace and special characters. This means that the output is treated as a single string.

Example:
```
result="$(ls -l)"
echo "$result"
```
In this case, the output of ls -l is stored in result with all its formatting preserved, including spaces and newlines.
No Quotes: If you do not use quotes, the shell performs word splitting and filename expansion on the output. This can lead to unexpected results if the output contains spaces or special characters.

Example:
```
result=$(ls -l)
echo $result
```
Here, the output of ls -l may be split into multiple arguments based on whitespace, which can lead to incorrect output or errors.

In summary, using quotes around command substitution helps to preserve the integrity of the output, ensuring that it is treated as a single entity, especially when it contains spaces or special characters.